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Crystal structure of the YbgO lectin domain, in complex with Man-alpha1-3-Man
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other YbgO apo
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 2M ammonium sulfate, 2M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.01 38.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.251 α = 93.156 b = 83.7 β = 89.962 c = 85.692 γ = 94.269
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2023-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.99 61.42 84.9 0.954 3.6 3.1 34053 10.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.06 0.528
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 61.42 1.92 33992 1730 66.72 0.2138 0.2116 0.2116 0.2553 0.2554 14.27
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.561 f_angle_d 1.1072 f_chiral_restr 0.0712 f_bond_d 0.0093 f_plane_restr 0.0085
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6116 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement autoPROC data processing PHASER phasing